[phenixbb] Dual conformation on symmetry axis

Tim Gruene tim.gruene at psi.ch
Fri Feb 5 00:35:06 PST 2016

Dear Jan,

density on symmetry elements usually displays artefacts and is difficult to 
interpret. If A clashes with A*, this is a real clash and you should not ask 
for this clash to be ignored.

Is this Arg biologically relevant? Otherwise, especially given the medium 
resolution, you probably create a better model by removing the side chain, 
even if that leaves difference density.


On Thursday, February 04, 2016 01:38:11 PM Jan Abendroth wrote:
> Hi all,
> I am running into the following problem during the refinement of a rather
> small structure at 2.15Å resolution:
> An Arg side chain is located very close to a crystallographic 2-fold. There
> is good evidence that the side chain has two conformations. However,
> because of the 2-fold, conformer A overlaps with its symmetry mate A*, as
> does conformer B. Phenix wants to avoid this 'clash' and moves A and A* out
> of the density, same for B and B*.
> Is there a way to avoid this without reducing the symmetry? In the real
> crystal, of course the two side chains are agnostic as to if they are
> called A or B and will avoid one another ...
> Thanks!
> Jan
> --
> Jan Abendroth
> Emerald Biostructures
> Seattle / Bainbridge Island, WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297


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